This study hypothesizes that the combination of atovaquone/azithromycin will be equivalent to or superior to trimethoprim/sulfamethoxazole for the prevention of serious bacterial infection in HIV-infected children with depleted CD4 lymphocyte populations. The long-term safety and tolerance of the two prophylactic regimens will also be evaluated as part of the study. After stratifying for previous use of TMP/SMX and/or IVIG, subjects were randomized to one of two arms: TMP/SMX (5 mg/kg/day) or micronized atovaquone (30 mg/kg/day) plus azithromycin (5 mg/kg/day). Cross-over to the alternative drug regimen was to occur if a serious treatment-related toxicity was observed. The efficacy of the antibacterial regimens is being evaluated through monitoring the occurrence of serious bacterial infections or PCP break-through. When a serious bacterial infection endpoint ( a second infection is identified) is reached, subjects will be crossed over to the alternative study drug regimen. Subjects will receive study drug until the last subject enrolled has completed 2 years follow up. The first 30 subjects were to have had a pharmacokinetics profile performed to assist in insuring that previously established blood concentrations of azithromycin and atovaquone were not significantly affected by the administration of the two drugs in combination.